For some reason, everytime I hit Update to update the tag, I get an error. When I get the error and look at the playlist, the file is updated, but when I reopen it, it just has the "?". This also happens with ReplayGaining wav files. When I goto "Show File Info", it shows the RG information, but when I go back in, it's gone.

How can I fix this?

Well, I'd guess you would probably either want to have a look at your input and database preferences

I'm quite sure it will be obvious then.

Hey and in case I'm wrong you can always come back and bitch at me for giving such a smartass answer

Oops. I'm sorry. I guess I should of looked. I found it! Sorry again.

No need to be sorry.

Reminder: WAV format doesn't have any widely-supported tagging standard, probably no other software will read APEv2 tags written by foobar2000, and some software may refuse to read tagged files at all (after all, APEv2 tags are not a part of WAV standard).
You can still remove those tags with new "Database/Remove tags from file" rightclick if you find a reason to do so.

They will just be used in foobar. I won't be burning them, so there is no real problem with tagging waves for me.

Perhaps the tags aren't part of the standard, but if I remember the RIFF file spec, a standards-compliant RIFF WAVE file reader ought to bypass them pretty well, shouldn't it?

Unless they contain hacks to bypass WAV file size limit (4GB), or check size reported by RIFF header against actual file size (and are so anal that they fail if it's smaller than actual size), they should.
I'd seriously use one of available lossless formats rather than plain WAV if I wanted to store original sound data. At least all of them have proper tagging that doesn't abuse their format specs.